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Imaging Neocortical Microcircuitry In Silico

Marwan Abdellah (Geneva 1202, Switzerland )

We developed methods to generate physically-realistic visualizations of neocortical models reconstructed by the Blue Brain Project. Current methods offer naïve, optical emission-only models that oversimplify light-tissue interaction. We visualise these models on a physically-plausible basis, taking into account the intrinsic optical properties of cortical tissue and the spectroscopic characteristics of its fluorescent structures. We present an efficient framework for creating high fidelity large-scale volumetric models of neocortical microcircuitry that govern the way in which light is distributed in cortical tissue. These models are reconstructed in two steps: first, we build piecewise watertight meshes of neocortical neurons from their morphological skeletons. Then, we apply solid voxelization to the meshes to build volumetric models. We also simulate imaging pipelines of transmitted light brightfield, widefield epi-fluorescence and light-sheet fluorescence microscopes. It is based on the principles of geometric optics and Monte Carlo ray tracing. We then exploit this framework to render in silico realistic microscopic images resembling those created by the actual instruments.